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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ), 'gf_id' => 'HOM05D001322', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001322' ), 'data_identifier' => 'HOM05D001322', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001322', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p11280' => 'bna', 'A07p13770' => 'bna', 'A07p13780' => 'bna', 'A08p28000' => 'bna', 'A09p41000' => 'bna', 'A10p10620' => 'bna', 'Aa31LG3G9350' => 'aar', 'Aa31LG7G7690' => 'aar', 'Aa31LG7G7700' => 'aar', 'Aa31LG7G7710' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.81' => 'aag', 'Actinidia01709' => 'ach', 'Actinidia08171' => 'ach', 'Actinidia08635' => 'ach', 'Actinidia15035' => 'ach', 'Ah.01g013570' => 'amhyb', 'Ah.03g132540' => 'amhyb', 'Ah.07g205930' => 'amhyb', 'AL1G37570' => 'aly', 'AL2G29610' => 'aly', 'AL8G27770' => 'aly', 'Aqoxy3G00968' => 'aox', 'Aqoxy3G03026' => 'aox', 'Aqoxy7G00117' => 'aox', 'arahy.Tifrunner.gnm1.ann1.397P62' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3EVA1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI1X3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7609CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BKDZ2C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CD11VG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY91G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GHL8IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUZX85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WC4CIS' => 'arhy', 'AT1G23820' => 'ath', 'AT1G70310' => 'ath', 'AT5G53120' => 'ath', 'ATR0188G012' => 'atr', 'ATR0691G088' => 'atr', 'ATR0691G300' => 'atr', 'ATR0751G162' => 'atr', 'Atru.chr1.143' => 'acertr', 'Atru.chr9.2440_Atru.chr9.2441' => 'acertr', 'AUR62005360' => 'cqu', 'AUR62006132' => 'cqu', 'AUR62009129' => 'cqu', 'AUR62014015' => 'cqu', 'AUR62019357' => 'cqu', 'AUR62039126' => 'cqu', 'AUR62044310' => 'cqu', 'BcaB03g11956' => 'bca', 'BcaB05g22013' => 'bca', 'BcaB07g32356' => 'bca', 'BcaB08g35671' => 'bca', 'BcaC03g14453' => 'bca', 'BcaC04g20503' => 'bca', 'BcaC05g26289' => 'bca', 'BcaC06g35053' => 'bca', 'BcaC06g35054' => 'bca', 'BcaC07g39216' => 'bca', 'BcaC07g39217' => 'bca', 'BcaC07g39218' => 'bca', 'BcaNung02491' => 'bca', 'BolC2t08009H' => 'bol', 'BolC5t30998H' => 'bol', 'BolC7t42545H' => 'bol', 'BolC7t42546H' => 'bol', 'BolC7t42547H' => 'bol', 'BolC8t49859H' => 'bol', 'BolC9t57158H' => 'bol', 'BraA02t06190Z' => 'bra', 'BraA07t29126Z' => 'bra', 'BraA07t29127Z' => 'bra', 'BraA08t34730Z' => 'bra', 'BraA09t39594Z' => 'bra', 'BraA10t43143Z' => 'bra', 'C02p18640' => 'bna', 'C05p22990' => 'bna', 'C05p43420' => 'bna', 'C07p20240' => 'bna', 'C07p20250' => 'bna', 'C08p22130' => 'bna', 'C09p42820' => 'bna', 'C09p74510' => 'bna', 'CAN.G108.44' => 'can', 'CAN.G1234.1' => 'can', 'CAN.G378.1' => 'can', 'CAN.G60.11' => 'can', 'CAN.G615.4' => 'can', 'CANSAT01G2608' => 'cansat', 'CANSAT21G1579' => 'cansat', 'CARHR024220' => 'chi', 'CARHR063450' => 'chi', 'CARHR063460' => 'chi', 'CARHR266150' => 'chi', 'Carub.0001s2332' => 'cru', 'Carub.0002s1699' => 'cru', 'Carub.0008s1332' => 'cru', 'Ca_04602_v3' => 'car', 'Ca_12692_v3' => 'car', 'Ca_16198_v3' => 'car', 'Ca_16689_v3' => 'car', 'Ca_22740_v3' => 'car', 'Ca_28611_v3' => 'car', 'Ca_30932_v3' => 'car', 'CBR_g36980' => 'cbr', 'CBR_g36983' => 'cbr', 'CBR_g45375' => 'cbr', 'Cc02_g01740' => 'ccan', 'Cc11_g14530' => 'ccan', 'CDE01G0244' => 'cde', 'CDE02G2940' => 'cde', 'CDE10G0118' => 'cde', 'CDE10G1134' => 'cde', 'Cfa009106' => 'cfa', 'Cfa019093' => 'cfa', 'Cfa026145' => 'cfa', 'Ciclev10006705m.g' => 'ccl', 'Ciclev10023140m.g' => 'ccl', 'Ciclev10024359m.g' => 'ccl', 'Ciclev10031988m.g' => 'ccl', 'CiPaw.03G231700' => 'cil', 'CiPaw.05G146600' => 'cil', 'CiPaw.05G255900' => 'cil', 'CiPaw.06G009600' => 'cil', 'CiPaw.06G074400' => 'cil', 'CiPaw.11G028900' => 'cil', 'CiPaw.12G025100' => 'cil', 'ClCG01G000500' => 'cla', 'ClCG01G013010' => 'cla', 'ClCG05G008810' => 'cla', 'ClCG05G025220' => 'cla', 'ClCG06G016890' => 'cla', 'COL.COLO4_04782' => 'col', 'COL.COLO4_34056' => 'col', 'COL.COLO4_36977' => 'col', 'COL.COLO4_38239' => 'col', 'Cpa.g.sc1551.1' => 'cpa', 'Cre12.g558450' => 'cre', 'CsaV3_1G001620' => 'csa', 'CsaV3_1G008360' => 'csa', 'CsaV3_1G008370' => 'csa', 'CsaV3_3G028000' => 'csa', 'CsaV3_5G000580' => 'csa', 'CsaV3_5G031670' => 'csa', 'CSS0000443' => 'camsi', 'CSS0004549' => 'camsi', 'CSS0006620' => 'camsi', 'CSS0007183' => 'camsi', 'CSS0016424' => 'camsi', 'CSS0029962' => 'camsi', 'CSS0032849' => 'camsi', 'CSS0044237' => 'camsi', 'DCAR_010607' => 'dca', 'DCAR_024141' => 'dca', 'DCAR_031094' => 'dca', 'Dinv05479' => 'din', 'Dinv15315' => 'din', 'Dinv24873' => 'din', 'Dinv35319' => 'din', 'Duzib068G0555' => 'dzi', 'Duzib068G0827' => 'dzi', 'Duzib205G0821' => 'dzi', 'Duzib205G1619' => 'dzi', 'Duzib248G0037' => 'dzi', 'Duzib268G1500' => 'dzi', 'ECA199G0008' => 'eca', 'ECA232G0869' => 'eca', 'ECA233G0891' => 'eca', 'ECA233G3495' => 'eca', 'EL10Ac3g05325' => 'bvu', 'EL10Ac6g13656' => 'bvu', 'Eucgr.A01487' => 'egr', 'Eucgr.B00355' => 'egr', 'Eucgr.C00527' => 'egr', 'Eucgr.H02622' => 'egr', 'FAN01G0681' => 'fan', 'FAN03G2740' => 'fan', 'FAN05G0635' => 'fan', 'FAN06G0038' => 'fan', 'FAN06G0578' => 'fan', 'FAN06G1996' => 'fan', 'FAN06G4671' => 'fan', 'FAN07G0982' => 'fan', 'FAN08G1214' => 'fan', 'FAN10G2653' => 'fan', 'FAN10G2745' => 'fan', 'FAN12G0262' => 'fan', 'FAN12G2107' => 'fan', 'FAN13G0054' => 'fan', 'FAN17G0882' => 'fan', 'FAN18G1385' => 'fan', 'FAN18G3478' => 'fan', 'FAN22G1376' => 'fan', 'FvH4_4g34680' => 'fve', 'FvH4_5g05120' => 'fve', 'FvH4_7g31820' => 'fve', 'FvH4_7g31860' => 'fve', 'Glyma.01G031700' => 'gma', 'Glyma.02G033900' => 'gma', 'Glyma.04G180500' => 'gma', 'Glyma.04G237300' => 'gma', 'Glyma.05G034900' => 'gma', 'Glyma.05G036300' => 'gma', 'Glyma.06G126700' => 'gma', 'Glyma.06G184100' => 'gma', 'Glyma.08G288100' => 'gma', 'Glyma.17G091100' => 'gma', 'Glyma.17G092400' => 'gma', 'Glyma.18G137100' => 'gma', 'Gohir.A03G140700' => 'ghi', 'Gohir.A07G060400' => 'ghi', 'Gohir.A08G096200' => 'ghi', 'Gohir.A08G195550' => 'ghi', 'Gohir.A12G251000' => 'ghi', 'Gohir.D02G163500' => 'ghi', 'Gohir.D07G065100' => 'ghi', 'Gohir.D08G103400' => 'ghi', 'Gohir.D12G251800' => 'ghi', 'Gorai.001G068600' => 'gra', 'Gorai.004G115100' => 'gra', 'Gorai.005G183500' => 'gra', 'Gorai.008G269900' => 'gra', 'GSVIVG01007787001' => 'vvi', 'GSVIVG01020222001' => 'vvi', 'GSVIVG01028700001' => 'vvi', 'HanXRQChr08g0208841' => 'han', 'HanXRQChr09g0252991' => 'han', 'HanXRQChr12g0371451' => 'han', 'HanXRQChr12g0383441' => 'han', 'HanXRQChr13g0393111' => 'han', 'HanXRQChr17g0570251' => 'han', 'Haze_00159' => 'cav', 'Haze_07491' => 'cav', 'Haze_12143' => 'cav', 'Haze_27347' => 'cav', 'Hma1.2p1_0160F.1_g070720' => 'hma', 'Hma1.2p1_0176F.1_g077700' => 'hma', 'Hma1.2p1_0538F.1_g174440' => 'hma', 'Hma1.2p1_0867F.1_g230310' => 'hma', 'HPP92_006485' => 'vpl', 'HPP92_006486' => 'vpl', 'HPP92_021641' => 'vpl', 'HPP92_021647' => 'vpl', 'HPP92_021729' => 'vpl', 'HPP92_027053' => 'vpl', 'HPP92_027412' => 'vpl', 'Hund05983' => 'sun', 'Hund11677' => 'sun', 'Hund25339' => 'sun', 'Lalb_Chr05g0216941' => 'lal', 'Lalb_Chr05g0227831' => 'lal', 'Lalb_Chr09g0326391' => 'lal', 'Lalb_Chr11g0066701' => 'lal', 'Lalb_Chr13g0297871' => 'lal', 'Lalb_Chr16g0382321' => 'lal', 'Lj1C1014G8' => 'lonja', 'Lj1g0001257' => 'lja', 'Lj2g0000085' => 'lja', 'Lj3C1051T11' => 'lonja', 'Lj4g0001598' => 'lja', 'Lj4g0025645' => 'lja', 'Lj4g0027516' => 'lja', 'Lj6C804T17' => 'lonja', 'Lsat_1_v5_gn_2_135921' => 'lsa', 'Lsat_1_v5_gn_3_87780' => 'lsa', 'Lsat_1_v5_gn_4_7021' => 'lsa', 'Lsat_1_v5_gn_8_158360' => 'lsa', 'Lsat_1_v5_gn_8_5021' => 'lsa', 'Lsat_1_v5_gn_9_58061' => 'lsa', 'Manes.06G103200' => 'mes', 'Manes.06G158700' => 'mes', 'Manes.12G030300' => 'mes', 'Manes.13G031400' => 'mes', 'Manes.14G007244' => 'mes', 'Manes.14G067700' => 'mes', 'Mapoly0038s0069' => 'mpo', 'Mapoly0116s0055' => 'mpo', 'MBI07_g23929_MAGBIO' => 'mbi', 'MBI07_g37610_MAGBIO' => 'mbi', 'MBI14_g43246_MAGBIO' => 'mbi', 'MCO02G091' => 'mco', 'MCO09G226' => 'mco', 'MD01G1221000' => 'mdo', 'MD01G1221200' => 'mdo', 'MD06G1177500' => 'mdo', 'MD07G1291100' => 'mdo', 'MD07G1292400' => 'mdo', 'MD13G1090400' => 'mdo', 'MD14G1183600' => 'mdo', 'MD16G1091000' => 'mdo', 'Medtr0044s0050' => 'mtr', 'Medtr1g028360' => 'mtr', 'Medtr3g078190' => 'mtr', 'Medtr3g091090' => 'mtr', 'Medtr5g034470' => 'mtr', 'Medtr8g063940' => 'mtr', 'MELO3C002252.2' => 'cme', 'MELO3C005877.2' => 'cme', 'MELO3C008477.2' => 'cme', 'MELO3C012007.2' => 'cme', 'MELO3C017103.2' => 'cme', 'Migut.E00155' => 'egut', 'Migut.F00231' => 'egut', 'Migut.L01398' => 'egut', 'MSTRG.2391' => 'ama', 'MSTRG.27038' => 'ama', 'MSTRG.603' => 'ama', 'Nitab4.5_0000013g0380' => 'nta', 'Nitab4.5_0000013g0390' => 'nta', 'Nitab4.5_0000034g0230' => 'nta', 'Nitab4.5_0000060g0100' => 'nta', 'Nitab4.5_0000113g0030' => 'nta', 'Nitab4.5_0000714g0010' => 'nta', 'Nitab4.5_0003284g0010' => 'nta', 'Nitab4.5_0003284g0040' => 'nta', 'Nitab4.5_0003646g0010' => 'nta', 'Nitab4.5_0004700g0060' => 'nta', 'Nitab4.5_0010954g0020' => 'nta', 'Nitab4.5_0011232g0010' => 'nta', 'Nitab4.5_0012491g0010' => 'nta', 'Nn1g01881' => 'nnu', 'Nn4g22824' => 'nnu', 'Oeu001676.1' => 'oeu', 'Oeu028911.1' => 'oeu', 'Oeu036105.1' => 'oeu', 'Oeu037103.2' => 'oeu', 'Os02g0254700' => 'osa', 'Os06g0528600' => 'osa', 'Os07g0408700' => 'osa', 'Peaxi162Scf00020g00055' => 'pax', 'Peaxi162Scf00075g01328' => 'pax', 'Peaxi162Scf00097g00233' => 'pax', 'Peaxi162Scf00198g00014' => 'pax', 'Peaxi162Scf00393g00010' => 'pax', 'Peaxi162Scf00442g00082' => 'pax', 'Peaxi162Scf00579g00211' => 'pax', 'Peaxi162Scf00589g00418' => 'pax', 'PGR042G2191' => 'pgr', 'PGR044G1464' => 'pgr', 'PGR083G2313' => 'pgr', 'PGR119G2185' => 'pgr', 'PGSC0003DMG400004111' => 'stu', 'PGSC0003DMG400009077' => 'stu', 'PGSC0003DMG400024232' => 'stu', 'PGSC0003DMG400036131' => 'stu', 'PGSC0003DMG400037026' => 'stu', 'Phvul.002G072200' => 'pvu', 'Phvul.003G052600' => 'pvu', 'Phvul.003G199000' => 'pvu', 'Phvul.009G054800' => 'pvu', 'Potri.008G147200' => 'ptr', 'Potri.010G094600' => 'ptr', 'Potri.012G002600' => 'ptr', 'Potri.015G018900' => 'ptr', 'Pp3c14_14230' => 'ppa', 'Pp3c17_5630' => 'ppa', 'Pp3c1_32030' => 'ppa', 'Pp3c2_2980' => 'ppa', 'PRCOL_00005760' => 'pco', 'Prupe.1G255300' => 'ppe', 'Prupe.2G312400' => 'ppe', 'Prupe.5G176100' => 'ppe', 'Prupe.5G176200' => 'ppe', 'Psat0s1463g0080' => 'psa', 'Psat2g103040' => 'psa', 'Psat5g077760' => 'psa', 'Psat5g113480' => 'psa', 'PSO017G2065' => 'pso', 'PSO063G5410' => 'pso', 'PSO063G6314' => 'pso', 'PSO170G6896' => 'pso', 'PSO384G4018' => 'pso', 'PSO478G2511' => 'pso', 'PSO675G1973' => 'pso', 'PSO728G0001' => 'pso', 'QL03p061719' => 'qlo', 'QL09p010247' => 'qlo', 'QL10p012202' => 'qlo', 'RcHm_v2.0_Chr1g0381051' => 'rch', 'RcHm_v2.0_Chr4g0444031' => 'rch', 'RcHm_v2.0_Chr7g0193881' => 'rch', 'Rhsim03G0201100' => 'rsi', 'Rhsim12G0047600' => 'rsi', 'Sabra08G0112000' => 'sbr', 'Sabra10G0066900' => 'sbr', 'Sabra12G0018900' => 'sbr', 'SalBow2G0312' => 'sbo', 'SalBow4G0680' => 'sbo', 'SalBow4G3105' => 'sbo', 'Sc04g0001900' => 'sci', 'Sc04g0009090' => 'sci', 'Sc19g0000900' => 'sci', 'Sed0001765' => 'sed', 'Sed0002842' => 'sed', 'Sed0009588' => 'sed', 'Sed0016425' => 'sed', 'Sed0020667' => 'sed', 'Sed0022756' => 'sed', 'SGA_v2.0_scaffold2010G54068' => 'sas', 'SGA_v2.0_scaffold236G43736' => 'sas', 'SGA_v2.0_scaffold44G16781' => 'sas', 'SGA_v2.0_scaffold63G21694' => 'sas', 'SHI17642' => 'shi', 'SHI17646' => 'shi', 'SMO144G0095' => 'smo', 'SMO356G0544' => 'smo', 'Solyc03g007240.3' => 'sly', 'Solyc04g026030.3' => 'sly', 'Solyc05g005710.4' => 'sly', 'Solyc06g053510.3' => 'sly', 'Solyc06g053520.4' => 'sly', 'Solyc08g014310.3' => 'sly', 'Sopen03g003220' => 'spe', 'Sopen04g013830' => 'spe', 'Sopen05g001710' => 'spe', 'Sopen06g018600' => 'spe', 'Sopen06g018610' => 'spe', 'Sopen08g005230' => 'spe', 'Sp1g21190' => 'spa', 'Sp5g25440' => 'spa', 'Sp6g15290' => 'spa', 'TAR365G0348' => 'tar', 'TAR365G0499' => 'tar', 'TAR365G1169' => 'tar', 'TAR371G0895' => 'tar', 'TAR375G0410' => 'tar', 'TAR375G0456' => 'tar', 'TAR622G0365' => 'tar', 'TAR622G1069' => 'tar', 'TAR629G0878' => 'tar', 'TAR629G2073' => 'tar', 'TAR636G0118' => 'tar', 'THA.LOC104800298' => 'tha', 'THA.LOC104822135' => 'tha', 'THA.LOC104822962' => 'tha', 'Thecc.02G244600' => 'tca', 'Thecc.03G008800' => 'tca', 'Thecc.03G008900' => 'tca', 'Thecc.03G009100' => 'tca', 'Thecc.03G194600' => 'tca', 'Thecc.04G007300' => 'tca', 'Thecc.10G102900' => 'tca', 'Thhalv10007822m.g' => 'esa', 'Thhalv10013929m.g' => 'esa', 'TPR.G13584' => 'tpr', 'TPR.G17289' => 'tpr', 'TPR.G29249' => 'tpr', 'TPR.G33298' => 'tpr', 'TPR.G33335' => 'tpr', 'TPR.G34959' => 'tpr', 'TPR.G7467' => 'tpr', 'TPR.G9478' => 'tpr', 'TWI14G0128' => 'twi', 'TWI18G0882' => 'twi', 'TWI36G0170' => 'twi', 'TWI36G0723' => 'twi', 'TWI39G0151' => 'twi', 'unitig_22.g6468' => 'ugi', 'unitig_25.g30563' => 'ugi', 'unitig_46.g18815' => 'ugi', 'unitig_8.g3170' => 'ugi', 'vmacro01185' => 'vma', 'vmacro06553' => 'vma', 'VMungo0251G3515' => 'vmu', 'VMungo1215G1029' => 'vmu', 'VMungo1215G3230' => 'vmu', 'VMungo1309G0718' => 'vmu', 'VMungo1309G2725' => 'vmu', 'Zm00001eb094730' => 'zma', 'Zm00001eb204260' => 'zma', 'Zm00001eb230230' => 'zma', 'Zm00001eb305710' => 'zma', 'Zm00001eb383120' => 'zma' ) $gf_id = 'HOM05D001322' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001322' ) $data_identifier = 'HOM05D001322' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 1, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 8, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 13, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 3, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383120' $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